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Ludtke SJ, He K, Heller WT, Harroun TA, Yang L, Huang HW. Membrane pores induced by magainin. Biochemistry 1996; 35:13723-8. [PMID: 8901513 DOI: 10.1021/bi9620621] [Citation(s) in RCA: 592] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data.
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Song CL, Wang YL, Cheng P, Jiang YP, Li W, Zhang T, Li Z, He K, Wang L, Jia JF, Hung HH, Wu C, Ma X, Chen X, Xue QK. Direct Observation of Nodes and Twofold Symmetry in FeSe Superconductor. Science 2011; 332:1410-3. [DOI: 10.1126/science.1202226] [Citation(s) in RCA: 333] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Zeng L, Ye Q, Oberlies NH, Shi G, Gu ZM, He K, McLaughlin JL. Recent advances in Annonaceous acetogenins. Nat Prod Rep 1996; 13:275-306. [PMID: 8760865 DOI: 10.1039/np9961300275] [Citation(s) in RCA: 274] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Review |
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Abstract
Magainin 2 is a 23-residue antibiotic peptide found in the skin of Xeonpus laevis (African clawed frog). It belongs to a broad class of alpha-helical peptides which interact directly with the lipid bilayer. Very little is presently known about the nature of this peptide/lipid interaction on the molecular level. We have performed a sequence of lamellar X-ray diffraction experiments to provide some insight into the nature of this interaction. We have found that, at concentrations below the critical concentration for lysis, the peptide causes the membrane thickness to decrease roughly in proportion to the peptide concentration. We further show that this thinning is consistent with a model where the peptide adsorbs within the headgroup region of the lipid bilayer at these concentrations. The energy cost of this thinning may also explain why the peptide inserts at high concentrations. We have already shown that a similar interaction exists for alamethicin interacting with diphytanoylphosphatidylcholine, and it should hold for a wide variety of peptide/lipid systems.
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He K, Hu FB, Colditz GA, Manson JE, Willett WC, Liu S. Changes in intake of fruits and vegetables in relation to risk of obesity and weight gain among middle-aged women. Int J Obes (Lond) 2005; 28:1569-74. [PMID: 15467774 DOI: 10.1038/sj.ijo.0802795] [Citation(s) in RCA: 246] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To examine the changes in intake of fruits and vegetables in relation to risk of obesity and weight gain among middle-aged women. DESIGN Prospective cohort study with 12 y of follow-up conducted in the Nurses' Health Study. SUBJECTS A total of 74,063 female nurses aged 38-63 y, who were free of cardiovascular disease, cancer, and diabetes at baseline in 1984. MEASUREMENTS Dietary information was collected using a validated food frequency questionnaire, and body weight and height were self-reported. RESULTS During the 12-y follow-up, participants tended to gain weight with aging, but those with the largest increase in fruit and vegetable intake had a 24% of lower risk of becoming obese (BMI> or =30 kg/m2) compared with those who had the largest decrease in intake after adjustment for age, physical activity, smoking, total energy intake, and other lifestyle variables (relative risk (RR), 0.76; 95% confidence interval (CI), 0.69-0.86; P for trend <0.0001). For major weight gain (> or =25 kg), women with the largest increase in intake of fruits and vegetables had a 28% lower risk compared to those in the other extreme group (RR, 0.72; 95% CI, 0.55-0.93; P=0.01). Similar results were observed for changes in intake of fruits and vegetables when analyzed separately. CONCLUSIONS Our findings suggest that increasing intake of fruits and vegetables may reduce long-term risk of obesity and weight gain among middle-aged women.
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Research Support, U.S. Gov't, P.H.S. |
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He K, Iyer KR, Hayes RN, Sinz MW, Woolf TF, Hollenberg PF. Inactivation of cytochrome P450 3A4 by bergamottin, a component of grapefruit juice. Chem Res Toxicol 1998; 11:252-9. [PMID: 9548795 DOI: 10.1021/tx970192k] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Grapefruit juice has been found to significantly increase oral bioavailability of several drugs metabolized by cytochrome P450 3A4 (P450 3A4) through inhibiting the enzymatic activity and decreasing the content of intestinal P450 3A4. HPLC/MS/MS and HPLC/UV analyses of ethyl acetate extracts from grapefruit juice revealed the presence of several furanocoumarins of which bergamottin (BG) is the major one. BG was shown to inactivate P450 3A4 in a reconstituted system consisting of purified P450 3A4, NADPH-cytochrome P450 reductase, cytochrome b5, and phospholipids. Inactivation was time- and concentration-dependent and required metabolism of BG. The loss of catalytic activity exhibited pseudo-first-order kinetics. The values of kinactivation and KI calculated from the inactivation studies were 0.3 min-1 and 7.7 microM, respectively. While approximately 70% of the erythromycin N-demethylation activity was lost during incubation with BG in the reconstituted system, P450 3A4 retained more than 90% of the heme as determined either by UV-visible spectroscopy or by HPLC. However, approximately 50% of the apoP450 in the BG-inactivated P450 3A4 incubation mixture could not be recovered from a reverse-phase HPLC column when compared with the -NADPH control. The mechanism of the inactivation appears to involve modification of the apoP450 in the active site of the enzyme instead of heme adduct formation or heme fragmentation. These results indicate that BG, the primary furanocoumarin extracted from grapefruit juice, is a mechanism-based inactivator of P450 3A4. BG was also found to inhibit the activities of P450s 1A2, 2A6, 2C9, 2C19, 2D6, 2E1, and 3A4 in human liver microsomes.
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Comparative Study |
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He K, Ludtke SJ, Worcester DL, Huang HW. Neutron scattering in the plane of membranes: structure of alamethicin pores. Biophys J 1996; 70:2659-66. [PMID: 8744303 PMCID: PMC1225245 DOI: 10.1016/s0006-3495(96)79835-1] [Citation(s) in RCA: 183] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A technique of neutron in-plane scattering for studying the structures of peptide pores in membranes is described. Alamethicin in the inserted state was prepared and undeuterated and deuterated dilauroyl phosphatidylcholine (DLPC) hydrated with D2O or H2O. Neutron in-plane scattering showed a strong dependence on deuteration, clearly indicating that water is a part of the high-order structure of inserted alamethicin. The data are consistent with the simple barrel-stave model originally proposed by Baumann and Mueller. The theoretical curves computed with this model at four different deuteration conditions agree with the data in all cases. Both the diameter of the water pore and the effective outside diameter of the channel are determined accurately. Alamethicin forms pores in a narrow range of size. In a given sample condition, > 70% of the peptide forms pores of n and n +/- 1 monomers. The pore size varies with hydration and with lipid. In DLPC, the pores are made of n = 8-9 monomers, with a water pore approximately 18 A in diameter and with an effective outside diameter of approximately 40 A. In diphytanoyl phosphatidylcholine, the pores are made of n approximately 11 monomers, with a water pore approximately 26 A in diameter, with an effective outside diameter of approximately 50 A.
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Zhang J, Chang CZ, Tang P, Zhang Z, Feng X, Li K, Wang LL, Chen X, Liu C, Duan W, He K, Xue QK, Ma X, Wang Y. Topology-Driven Magnetic Quantum Phase Transition in Topological Insulators. Science 2013; 339:1582-6. [DOI: 10.1126/science.1230905] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Abstract
Alamethicin adsorbs on the membrane surface at low peptide concentrations. However, above a critical peptide-to-lipid ratio (P/L), a fraction of the peptide molecules insert in the membrane. This critical ratio is lipid dependent. For diphytanoyl phosphatidylcholine it is about 1/40. At even higher concentrations P/L > or = 1/15, all of the alamethicin inserts into the membrane and forms well-defined pores as detected by neutron in-plane scattering. A previous x-ray diffraction measurement showed that alamethicin adsorbed on the surface has the effect of thinning the bilayer in proportion to the peptide concentration. A theoretical study showed that the energy cost of membrane thinning can indeed lead to peptide insertion. This paper extends the previous studies to the high-concentration region P/L > 1/40. X-ray diffraction shows that the bilayer thickness increases with the peptide concentration for P/L > 1/23 as the insertion approaches 100%. The thickness change with the percentage of insertion is consistent with the assumption that the hydrocarbon region of the bilayer matches the hydrophobic region of the inserted peptide. The elastic energy of a lipid bilayer including both adsorption and insertion of peptide is discussed. The Gibbs free energy is calculated as a function of P/L and the percentage of insertion phi in a simplified one-dimensional model. The model exhibits an insertion phase transition in qualitative agreement with the data. We conclude that the membrane deformation energy is the major driving force for the alamethicin insertion transition.
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Yaemsiri S, Hou N, Slining MM, He K. Growth rate of human fingernails and toenails in healthy American young adults. J Eur Acad Dermatol Venereol 2010; 24:420-3. [DOI: 10.1111/j.1468-3083.2009.03426.x] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wu Y, He K, Ludtke SJ, Huang HW. X-ray diffraction study of lipid bilayer membranes interacting with amphiphilic helical peptides: diphytanoyl phosphatidylcholine with alamethicin at low concentrations. Biophys J 1995; 68:2361-9. [PMID: 7647240 PMCID: PMC1282146 DOI: 10.1016/s0006-3495(95)80418-2] [Citation(s) in RCA: 160] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A variety of amphiphilic helical peptides have been shown to exhibit a transition from adsorbing parallel to a membrane surface at low concentrations to inserting perpendicularly into the membrane at high concentrations. Furthermore, this transition has been correlated to the peptides' cytolytic activities. X-ray lamellar diffraction of diphytanoyl phosphatidylcholine-alamethicin mixtures revealed the changes of the bilayer structure with alamethicin concentration. In particular, the bilayer thickness decreases with increasing peptide concentration in proportion to the peptide-lipid molar ratio from as low as 1:150 to 1:47; the latter is near the threshold of the critical concentration for insertion. From the decreases of the bilayer thickness, one can calculate the cross sectional expansions of the lipid chains. For all of the peptide concentrations studied, the area expansion of the chain region for each adsorbed peptide is a constant 280 +/- 20 A2, which is approximately the cross sectional area of an adsorbed alamethicin. This implies that the peptide is adsorbed at the interface of the hydrocarbon region, separating the lipid headgroups laterally. Interestingly, the chain disorder caused by a peptide adsorption tends to spread over a large area, as much as 100 A in diameter. The theoretical basis of the long range nature of bilayer deformation is discussed.
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Song Y, He K, Levitan EB, Manson JE, Liu S. Effects of oral magnesium supplementation on glycaemic control in Type 2 diabetes: a meta-analysis of randomized double-blind controlled trials. Diabet Med 2006; 23:1050-6. [PMID: 16978367 DOI: 10.1111/j.1464-5491.2006.01852.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
AIMS The aim of this study was to assess the evidence on the effect of oral magnesium supplementation on glycaemic control in patients with Type 2 diabetes. METHODS We searched the electronic databases of medline, embase and the Cochrane Controlled Trials Register up to January 2005. We identified nine randomized double-blind controlled trials with a total of 370 patients with Type 2 diabetes and of duration 4-16 weeks. The median dose of oral magnesium supplementation was 15 mmol/day (360 mg/day) in the treatment groups. The primary outcome was glycaemic control, as measured by glycated haemoglobin (HbA(1c)) or fasting blood glucose levels; the secondary outcomes included body mass index, blood pressure (BP) and lipids. Using a random-effects model, we calculated the weighted mean differences (WMD) and 95% confidence interval (CI). RESULTS After a median duration of 12 weeks, the weighted mean post-intervention fasting glucose was significantly lower in the treatment groups compared with the placebo groups [-0.56 mmol/l (95% CI, -1.10 to -0.01); P for heterogeneity = 0.02]. The difference in post-intervention HbA(1c) between magnesium supplementation groups and control groups was not significant [-0.31% (95% CI, -0.81 to 0.19); P for heterogeneity = 0.10]. Neither systolic nor diastolic BP was significantly changed. Magnesium supplementation increased on high-density lipoprotein (HDL) cholesterol levels [0.08 mmol/l (95% CI, 0.03 to 0.14); P for heterogeneity = 0.36] but had no effect on total cholesterol, low-density lipoprotein (LDL) cholesterol and triglyceride. CONCLUSIONS Oral magnesium supplementation for 4-16 weeks may be effective in reducing plasma fasting glucose levels and raising HDL cholesterol in patients with Type 2 diabetes, although the long-term benefits and safety of magnesium treatment on glycaemic control remain to be determined.
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Meta-Analysis |
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Zheng BL, He K, Kim CH, Rogers L, Shao Y, Huang ZY, Lu Y, Yan SJ, Qien LC, Zheng QY. Effect of a lipidic extract from lepidium meyenii on sexual behavior in mice and rats. Urology 2000; 55:598-602. [PMID: 10736519 DOI: 10.1016/s0090-4295(99)00549-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVES To determine the effect of oral administration of a purified lipidic extract from Lepidium meyenii (MacaPure M-01 and M-02) on the number of complete intromissions and mating in normal mice, and on the latent period of erection (LPE) in rats with erectile dysfunction. METHODS Mice and rats were randomly divided into several experimental and control groups. A 10% ethanol suspension of M-01 and M-02 was orally administered for 22 days to the experimental groups according to the dosage specified by the experimental design. On day 22, 30 minutes after the dose was administered to the male mice, 2 virgin female mice were placed with 1 male mouse. The number of complete intromissions of each male mouse in 3 hours was recorded. In an assessment of 1 day of mating, each male mouse was cohabited with 5 estrous female mice overnight. The number of sperm-positive females was recorded. The LPE was measured to assess the sexual function in rats with erectile dysfunction. By using a YSD-4G multifunction instrument, an electric pulse at 20 V was applied to stimulate the rat's penis, and the duration from the start of the stimulus to full erection was measured in seconds as the LPE. RESULTS In the normal male mice, the number of complete intromissions during the 3-hour period was 16.33 +/- 1.78, 46.67 +/- 2.39, and 67.01 +/- 2.55 for the control group, M-01 group, and M-02 group, respectively. In the assessment of mating, the number of sperm-positive females increased from 0.6 +/- 0.7 in the control group to 1.5 +/- 0.5 in the M-01 experimental group. The LPE of male rats with erectile dysfunction was 112 +/- 13 seconds with a regular diet (control group). The oral administration of M-01 at a dose of 180 or 1800 mg/kg body weight and M-02 at a dose of 45, 180, or 1800 mg/kg body weight reduced the LPE to 54 +/- 12 seconds, 54 +/- 13 seconds, 71 +/- 12 seconds, 73 +/- 12 seconds, and 41 +/- 13 seconds, respectively. The LPE of the surgical rats treated with M-01 at the lowest dose (45 mg/kg) was 121 +/- 12 seconds; thus, the change was not significant. CONCLUSIONS Oral administration of M-01 and M-02 enhanced the sexual function of the mice and rats, as evidenced by an increase in the number of complete intromissions and the number of sperm-positive females in normal mice, and a decrease in the LPE in male rats with erectile dysfunction. The present study reveals for the first time an aphrodisiac activity of L. meyenii, an Andean Mountain herb.
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Ludtke SJ, He K, Wu Y, Huang HW. Cooperative membrane insertion of magainin correlated with its cytolytic activity. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1190:181-4. [PMID: 8110813 DOI: 10.1016/0005-2736(94)90050-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using oriented circular dichroism, we have found that magainin adopts an alpha-helical conformation with two distinct orientations when interacting with a lipid bilayer. At low concentrations, magainin is absorbed parallel to the membrane surface. However, at high concentrations, magainin is inserted into the membrane. This transition occurs at roughly the same critical concentration required for cytolytic activity, implying that the membrane insertion is responsible for magainin's cell-lysing activity.
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He K, Ludtke SJ, Huang HW, Worcester DL. Antimicrobial peptide pores in membranes detected by neutron in-plane scattering. Biochemistry 1995; 34:15614-8. [PMID: 7495788 DOI: 10.1021/bi00048a002] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Antimicrobial peptides isolated from the host defense systems of animals have been shown to exert their activity directly on the lipid bilayer of cell membranes, but the antimicrobial mechanisms are not clear, due chiefly to the difficulty of discerning the high-order structures formed by these peptides in membranes. Previously we have shown that these peptides insert into the membrane when their concentrations exceed a lipid-dependent critical value. With neutron in-plane scattering we now show that inserted alamethicin creates aqueous pores approximately greater than 18 A in diameter. The density of pores is consistent with the assumption that all of the alamethicin is involved in pore formation. Pores were not detected below the critical concentration. Thus concentration-dependent pore formation appears to be the molecular mechanism of antimicrobial action.
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Koka P, He K, Zack JA, Kitchen S, Peacock W, Fried I, Tran T, Yashar SS, Merrill JE. Human immunodeficiency virus 1 envelope proteins induce interleukin 1, tumor necrosis factor alpha, and nitric oxide in glial cultures derived from fetal, neonatal, and adult human brain. J Exp Med 1995; 182:941-51. [PMID: 7561697 PMCID: PMC2192278 DOI: 10.1084/jem.182.4.941] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Although microglia are the only cells found to be productively infected in the central nervous system of acquired immunodeficiency disease syndrome (AIDS) patients, there is extensive white and gray matter disease nonetheless. This neuropathogenesis is believed to be due to indirect mechanisms other than infection with human immunodeficiency virus 1 (HIV-1). Cytokines and toxic small molecules have been implicated in the clinical and histopathological findings in CNS AIDS. Previously, we have demonstrated in rodent glial cultures the presence of biologically active epitopes of gp120 and gp41 that are capable of inducing interleukin 1 and tumor necrosis factor alpha. In this study, we map the HIV-1 envelope epitopes that induce nitric oxide, inducible nitric oxide synthase, interleukin 1, and tumor necrosis factor alpha in human glial cultures. Epitopes in the carboxy terminus of gp120 and the amino terminus of gp41 induce these proinflammatory entities. In addition, we compare HIV-1 infection and pathology in glial cells derived from human brain taken at different states of maturation (fetal, neonatal, and adult brain) in an effort to address some of the clinical and histological differences seen in vivo. This study demonstrates that, in the absence of virus infection and even in the absence of distinct viral tropism, human glia respond like rodent glia to non-CD4-binding epitopes of gp120/gp41 with cytokine and nitric oxide production. Differences among fetal, neonatal, and adult glial cells' infectivity and cytokine production indicate that, in addition to functional differences of glia at different stages of development, cofactors in vitro and in vivo may also be critical in facilitating the biological responses of these cells to HIV-1.
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Heller WT, He K, Ludtke SJ, Harroun TA, Huang HW. Effect of changing the size of lipid headgroup on peptide insertion into membranes. Biophys J 1997; 73:239-44. [PMID: 9199788 PMCID: PMC1180925 DOI: 10.1016/s0006-3495(97)78064-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Adsorption of amphiphilic peptides to the headgroup region of a lipid bilayer is a common mode of protein-membrane interactions. Previous studies have shown that adsorption causes membrane thinning. The degree of the thinning depends on the degree of the lateral expansion caused by the peptide adsorption. If this simple molecular mechanism is correct, the degree of lateral expansion and consequently the membrane thinning should depend on the size of the headgroup relative to the cross section of the hydrocarbon chains. Previously we have established the connection between the alamethicin insertion transition and the membrane thinning effect. In this paper we use oriented circular dichroism to study the effect of varying the size of the headgroup, while maintaining a constant cross section of the lipid chains, on the insertion transition. A simple quantitative prediction agrees very well with the experiment.
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Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
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Review |
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Albrechtsen A, Grarup N, Li Y, Sparsø T, Tian G, Cao H, Jiang T, Kim SY, Korneliussen T, Li Q, Nie C, Wu R, Skotte L, Morris AP, Ladenvall C, Cauchi S, Stančáková A, Andersen G, Astrup A, Banasik K, Bennett AJ, Bolund L, Charpentier G, Chen Y, Dekker JM, Doney ASF, Dorkhan M, Forsen T, Frayling TM, Groves CJ, Gui Y, Hallmans G, Hattersley AT, He K, Hitman GA, Holmkvist J, Huang S, Jiang H, Jin X, Justesen JM, Kristiansen K, Kuusisto J, Lajer M, Lantieri O, Li W, Liang H, Liao Q, Liu X, Ma T, Ma X, Manijak MP, Marre M, Mokrosiński J, Morris AD, Mu B, Nielsen AA, Nijpels G, Nilsson P, Palmer CNA, Rayner NW, Renström F, Ribel-Madsen R, Robertson N, Rolandsson O, Rossing P, Schwartz TW, Slagboom PE, Sterner M, Tang M, Tarnow L, Tuomi T, van’t Riet E, van Leeuwen N, Varga TV, Vestmar MA, Walker M, Wang B, Wang Y, Wu H, Xi F, Yengo L, Yu C, Zhang X, Zhang J, Zhang Q, Zhang W, Zheng H, Zhou Y, Altshuler D, ‘t Hart LM, Franks PW, Balkau B, Froguel P, McCarthy MI, Laakso M, Groop L, Christensen C, Brandslund I, Lauritzen T, Witte DR, et alAlbrechtsen A, Grarup N, Li Y, Sparsø T, Tian G, Cao H, Jiang T, Kim SY, Korneliussen T, Li Q, Nie C, Wu R, Skotte L, Morris AP, Ladenvall C, Cauchi S, Stančáková A, Andersen G, Astrup A, Banasik K, Bennett AJ, Bolund L, Charpentier G, Chen Y, Dekker JM, Doney ASF, Dorkhan M, Forsen T, Frayling TM, Groves CJ, Gui Y, Hallmans G, Hattersley AT, He K, Hitman GA, Holmkvist J, Huang S, Jiang H, Jin X, Justesen JM, Kristiansen K, Kuusisto J, Lajer M, Lantieri O, Li W, Liang H, Liao Q, Liu X, Ma T, Ma X, Manijak MP, Marre M, Mokrosiński J, Morris AD, Mu B, Nielsen AA, Nijpels G, Nilsson P, Palmer CNA, Rayner NW, Renström F, Ribel-Madsen R, Robertson N, Rolandsson O, Rossing P, Schwartz TW, Slagboom PE, Sterner M, Tang M, Tarnow L, Tuomi T, van’t Riet E, van Leeuwen N, Varga TV, Vestmar MA, Walker M, Wang B, Wang Y, Wu H, Xi F, Yengo L, Yu C, Zhang X, Zhang J, Zhang Q, Zhang W, Zheng H, Zhou Y, Altshuler D, ‘t Hart LM, Franks PW, Balkau B, Froguel P, McCarthy MI, Laakso M, Groop L, Christensen C, Brandslund I, Lauritzen T, Witte DR, Linneberg A, Jørgensen T, Hansen T, Wang J, Nielsen R, Pedersen O. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia 2013; 56:298-310. [PMID: 23160641 PMCID: PMC3536959 DOI: 10.1007/s00125-012-2756-1] [Show More Authors] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 09/28/2012] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Human complex metabolic traits are in part regulated by genetic determinants. Here we applied exome sequencing to identify novel associations of coding polymorphisms at minor allele frequencies (MAFs) >1% with common metabolic phenotypes. METHODS The study comprised three stages. We performed medium-depth (8×) whole exome sequencing in 1,000 cases with type 2 diabetes, BMI >27.5 kg/m(2) and hypertension and in 1,000 controls (stage 1). We selected 16,192 polymorphisms nominally associated (p < 0.05) with case-control status, from four selected annotation categories or from loci reported to associate with metabolic traits. These variants were genotyped in 15,989 Danes to search for association with 12 metabolic phenotypes (stage 2). In stage 3, polymorphisms showing potential associations were genotyped in a further 63,896 Europeans. RESULTS Exome sequencing identified 70,182 polymorphisms with MAF >1%. In stage 2 we identified 51 potential associations with one or more of eight metabolic phenotypes covered by 45 unique polymorphisms. In meta-analyses of stage 2 and stage 3 results, we demonstrated robust associations for coding polymorphisms in CD300LG (fasting HDL-cholesterol: MAF 3.5%, p = 8.5 × 10(-14)), COBLL1 (type 2 diabetes: MAF 12.5%, OR 0.88, p = 1.2 × 10(-11)) and MACF1 (type 2 diabetes: MAF 23.4%, OR 1.10, p = 8.2 × 10(-10)). CONCLUSIONS/INTERPRETATION We applied exome sequencing as a basis for finding genetic determinants of metabolic traits and show the existence of low-frequency and common coding polymorphisms with impact on common metabolic traits. Based on our study, coding polymorphisms with MAF above 1% do not seem to have particularly high effect sizes on the measured metabolic traits.
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Dibaba DT, Xun P, He K. Dietary magnesium intake is inversely associated with serum C-reactive protein levels: meta-analysis and systematic review. Eur J Clin Nutr 2014; 68:510-6. [PMID: 24518747 PMCID: PMC3975661 DOI: 10.1038/ejcn.2014.7] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/11/2013] [Accepted: 09/13/2013] [Indexed: 12/15/2022]
Abstract
BACKGROUND/OBJECTIVES The aim of this study was to quantitatively summarize the association of dietary magnesium (Mg) intake with serum C-reactive protein (CRP) levels in the general population. SUBJECTS/METHODS Observational and experimental studies through February 2013 were reviewed in PubMed and EMBASE. Additional information was retrieved through Google or hand search of related reference lists. The main outcome is either adjusted geometric mean of CRP or odds ratio (OR) of having serum CRP ≥ 3 mg/l. Meta-regression was used to determine the linear association of dietary Mg intake and adjusted geometric means of CRP levels. A fixed-effects model was used to pool ORs of interest, comparing those in the lowest with those in the highest group of dietary Mg intake. RESULTS A data set derived from seven cross-sectional studies including 32,918 participants was quantitatively assessed. A weighted inverse association between Mg intake and serum CRP levels was observed (β-coefficient: -0.0028; 95% confidence interval (CI), -0.0043 to -0.0013; P(trend) = 0.001) from four cross-sectional studies. The pooled OR (95% CI) of having CRP ≥ 3 mg/l was 1.49 (1.18-1.89) on comparing the lowest to the highest group of Mg intake from three studies with the data available. Qualitative assessment among five intervention studies also showed a potential beneficial effect of Mg intake on serum CRP levels. CONCLUSIONS This meta-analysis and systematic review indicates that dietary Mg intake is significantly and inversely associated with serum CRP levels. The potential beneficial effect of Mg intake on chronic diseases may be, at least in part, explained by inhibiting inflammation.
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Systematic Review |
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Lu L, Xun P, Wan Y, He K, Cai W. Long-term association between dairy consumption and risk of childhood obesity: a systematic review and meta-analysis of prospective cohort studies. Eur J Clin Nutr 2016; 70:414-23. [PMID: 26862005 DOI: 10.1038/ejcn.2015.226] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 10/29/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND/OBJECTIVES Data from small-scale, short-term, clinical trials suggest a beneficial effect of dairy consumption on the risk of childhood obesity; however, the long-term association is unclear. Therefore, we aim to examine the longitudinal association between dairy consumption and the risk of overweight/obesity in children and adolescents by conducting a systematic review and meta-analysis of prospective cohort studies. SUBJECTS/METHODS Eligible studies were identified by searching PubMed and EMBASE through March 2015. Additional studies were retrieved via Google Scholar or a hand review of the reference lists from relevant articles. Pooled associations of interest were estimated by using a random-effects model. The heterogeneity for each pooled analysis was evaluated by I(2) statistic as well as by Cochran's Q test. Publication bias was assessed by using both Egger's and Begg's tests. RESULTS Ten studies comprising 46,011 children and adolescents with an average 3-year follow-up were included. As compared with those who were in the lowest group of dairy consumption, children in the highest intake group were 38% less likely to have childhood overweight/obesity (pooled odds ratio (OR)=0.62; 95% confidence interval (CI): 0.49, 0.80). With each 1 serving/day increment in dairy consumption, the percentage of body fat was reduced by 0.65% (β=0.65; 95% CI: -1.35, 0.06; P=0.07), and the risk of overweight/obesity was 13% lower (OR=0.87; 95% CI: 0.74, 0.98). CONCLUSIONS Accumulated evidence from prospective cohort studies suggests that dairy consumption is inversely and longitudinally associated with the risk of childhood overweight/obesity. Further studies are warranted to examine the types of dairy products in relation to the risk of childhood overweight/obesity.
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Systematic Review |
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He K, Zheng X, Li M, Zhang L, Yu J. mTOR inhibitors induce apoptosis in colon cancer cells via CHOP-dependent DR5 induction on 4E-BP1 dephosphorylation. Oncogene 2015; 35:148-57. [PMID: 25867072 PMCID: PMC4603992 DOI: 10.1038/onc.2015.79] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/30/2014] [Accepted: 02/05/2015] [Indexed: 12/29/2022]
Abstract
The mammalian target of rapamycin (mTOR) is commonly activated in colon cancer. mTOR complex 1 (mTORC1) is a major downstream target of the PI3K/ATK pathway and activates protein synthesis by phosphorylating key regulators of mRNA translation and ribosome synthesis. Rapamycin analogs Everolimus and Temsirolimus are non-ATP-competitive mTORC1 inhibitors, and suppress proliferation and tumor angiogenesis and invasion. We now show that apoptosis plays a key role in their anti-tumor activities in colon cancer cells and xenografts through the DR5, FADD and caspase-8 axis, and is strongly enhanced by TRAIL and 5-fluorouracil. The induction of DR5 by rapalogs is mediated by the ER stress regulator and transcription factor CHOP, but not the tumor suppressor p53, upon rapid and sustained inhibition of 4E-BP1 phosphorylation, and attenuated by eIF4E expression. ATP-competitive mTOR/PI3K inhibitors also promote DR5 induction and FADD-dependent apoptosis in colon cancer cells. These results establish activation of ER stress and the death receptor pathway as a novel anticancer mechanism of mTOR inhibitors.
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Liu H, Sun F, He K, Sun Z. Design of Reduced-Order<tex>$ cal H_infty $</tex>Filter for Markovian Jumping Systems With Time Delay. ACTA ACUST UNITED AC 2004. [DOI: 10.1109/tcsii.2004.836882] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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He K, Zeng L, Shi G, Zhao GX, Kozlowski JF, McLaughlin JL. Bioactive compounds from Taiwania cryptomerioides. JOURNAL OF NATURAL PRODUCTS 1997; 60:38-40. [PMID: 9014350 DOI: 10.1021/np960513c] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two new sesquiterpenes, 10 alpha-hydroxyamorphan-4-en-3-one (1) and 4 alpha-methylcadinane-4 alpha-methyl-1 alpha,2 alpha,10 alpha-triol (2), together with four known compounds, sesquiterpenes 10 alpha-hydroxycadinan-4-en-3-one (3) and alpha-cadinol (4), diterpene ferruginol and lignan helioxanthin, were isolated from the whole plant of Taiwania cryptomerioides under bioassay-guided fractionations. The structures of 1 and 2 were elucidated mainly by the NMR spectroscopic analyses. Bioactivities of the isolated compounds against brine shrimp, yellow fever mosquito larvae, and human tumor cells are reported; compound 4 was the most bioactive, showing selectivity for the human colon tumor cell line (HT-29).
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He XY, Xiao L, Chen HB, Hao J, Li J, Wang YJ, He K, Gao Y, Shi BY. T regulatory cells and Th1/Th2 cytokines in peripheral blood from tuberculosis patients. Eur J Clin Microbiol Infect Dis 2010; 29:643-50. [PMID: 20306324 DOI: 10.1007/s10096-010-0908-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 02/20/2010] [Indexed: 02/07/2023]
Abstract
About 10% of people infected with Mycobacterium tuberculosis develop active tuberculosis (TB), and Th1 effector cells and Th1 cytokines play key roles in controlling M. tuberculosis infection. Here, we hypothesise that this susceptibility to M. tuberculosis infection is linked to increased T regulatory (Treg) cells and Th2 cytokines in TB patients. To test this, we recruited 101 participants (71 TB patients, 12 non-TB pulmonary diseases and 18 healthy subjects) and investigated Treg cells and Th1/Th2 cytokines in peripheral blood. CD4(+)CD25(+) T cells and CD4(+)CD25(+)FoxP3(+) T cells significantly increased and IL-5 dramatically decreased in TB patients relative to healthy subjects. CD8(+)CD28(-) T cells, IFN-gamma, TNF-alpha, IL-10 and IL-4 significantly increased in patients with culture and sputum smear-positive pulmonary TB (PTB(+)) compared with healthy subjects. CD4(+)CD25(+)FoxP3(+) and CD8(+)CD28(-) T cells significantly decreased in PTB(+) after one month of chemotherapy. CD4(+), CD4(+)CD25(+) and CD8(+)CD28(+) T cells significantly increased in extra-pulmonary TB patients after one month of chemotherapy. These findings suggest that M. tuberculosis infection induces circulating CD4(+)CD25(+)FoxP3(+) and CD8(+)CD28(-) T cell expansion, which may be related to the progression of M. tuberculosis infection, and that the balance between effector immune responses and suppression immune responses is essential to control M. tuberculosis infection.
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Research Support, Non-U.S. Gov't |
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